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simple_cycpep_predict - Design mode - The base name "ARG" was added more than once

Category: 
Design

Hello,

I am using simple_cycpep_predict in design mode to find derivatives of a peptide for disulfide cyclization. For the -cyclic_peptide:allowed_residues_by_position option I am using the following file:

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Academic email

Category: 
ROSIE

I encountered this error while trying to login to ROSIE:Your GitHub account does not have verified academic email address! My academic domain ( @kribb.re.kr ) cannot be verified during login to rosie. My institution is public research organization in south Korea

Thank

Post Situation: 

RIFdocking:Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/

Category: 
Design

Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows:

cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent

After the command is run, I got the following error:

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Renumbering PDB

Category: 
Docking

Hello,

I have been running this command other pdbs:

python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/pdb_renumber.py \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb

and it has worked. Yet when I run it for my current pdb, it produces this error:

Post Situation: 

Ensemble Docking with RosettaDock 4.0 Protocol

Category: 
Docking

Greetings,

I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:

$ mpirun -np 24 --hostfile $PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags

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"corrupted" small molecules. aromatic rings get distortet during relax

Category: 
PyRosetta

Hello, i am trying to relax an enzyme with a co-factor (nadp) but whenever I do, the resulting structure looks wrong.

I use the NADP structure from pubchem as a starting point, then molfile2params structure  and copy paste the returned LG_0001.pdb to my protein. 

i then run the following code:

Post Situation: 

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